Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcgggactgtattgacacgcttctttgttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcggg--actgtat-tgacacgcttctttg--ttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
| | | | | | | | ||| || ||| || ||| || | || | | |||| |||||||||||| ||| |||| ||||||||||| ||||| |||| ||| ||||| |||||||||||||||||
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgatttcatccttaatcatt--cttattcgggactgtattgacacgcttctttgttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
| || || | | || || | | | ||| || ||| | | ||| ||| | || ||| |||| ||||||| ||| |||| ||||||||||| ||||| |||| ||| ||||| |||||||||||||||||
gtactaattgttttgtgttctgattcaatgttcatttgtttctgattgcggacaaattgttgatttccttgcctgcgagat-tagatttgtcggaaactaagccttgtg-tgaatgtttagctttctagatacttaatttaacgtgttatttttttttatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTACATCCAACAGAGCCATG
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcgg--gactgtattgacacgcttctttgt-tttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
|| || || | || || | | | || | | || | | | ||| ||| | | ||||| ||||| ||| |||| ||||||||||| ||||| || ||||| ||||| ||||||||||| |||||
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgattt--catccttaatcattcttattcgggactgtattgacacgcttctttgt--tttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
|| || | || || | | || || || || | || | | ||| | || | ||||| ||||| ||| |||| ||||||||||| ||||| || ||||| ||||| ||||||||||| |||||
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtaatgcagtctcctttgatgctcgatttca---tccttaatcattcttattcgggactgtattgacacgcttctttg-------ttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
| | || ||| | | | ||| || | ||||| || || | | | || || | ||| ||| |||||| | || | || ||||||||||| ||||| |||||||| ||||| |||||| | ||||||||
gtacgcttgtttattccctttgaattgatttctatgtacagattagatctcgatttgtttaatgtttaatagttgaagtattgatgtcattttgcttctggtaaattttggatcagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccttaatcattcttattcgggactgtattgacacgcttctttgttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
tattgac putative branch site (score: 2)
cgcttctttgtttt CT-rich tract
taatcattcttatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcgggactgtattgacacgcttctttgttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA